�����ƽ��

The Dek histone chaperone promotes mammary gland development through the regulation of proliferation-driving cell cycle genes and deposition of H3K27me3 epigenetic marks. The DEK chromatin remodeling protein has oncogenic functions in breast cancers, but its functional role in normal mammary gland epithelium has remained unexplored. We developed two novel genetically engineered mouse models to study the role of Dek in normal mammary gland biology in vivo. Mammary gland-specific Dek transgenic mice developed hyperplasia and had a transcriptional profile that revealed increased expression of cell cycle, mammary stem/progenitor, and lactation-associated genes. Conversely, Dek knockout mice exhibited mammary gland functional defects resulting in dramatically reduced pup survival. Analysis of previously published scRNA-sequencing of mouse mammary glands revealed that Dek is most highly expressed in mammary stem cells and alveolar progenitor cells, supporting the observed phenotypes. Mechanistically, we discovered that Dek is a modifier of Ezh2 methyltransferase activity, up-regulating the levels of histone H3K27me3 to control gene transcription. Combined, this is the first report to show that Dek promotes proliferation of mammary epithelial cells via transcriptional deregulation of cell cycle genes, potentially via epigenetic mechanisms, in vivo.

Single-cell profiling protein-chromatin interactions is often constrained by complex workflows, high cost, or dependence on specialized equipment. We present indexed tagmentation-based single-cell CUT&Tag-sequencing (IT-scC&T-seq), a modular, plate-based strategy using three-round combinatorial barcoding. IT-scC&T-seq robustly profiles histone modifications and transcription factors with high specificity and throughput, supporting simultaneous analysis of multiple samples and epitopes. Notably, it enables sensitive single-cell mapping of lamina-associated domains, low-abundance chromatin features previously difficult to resolve. Applied to adult mouse mammary gland, the method reveals cell-type-specific chromatin landscapes and lineage-regulatory dynamics. Together, IT-scC&T-seq provides a scalable, cost-effective, and broadly accessible approach for high-resolution chromatin profiling.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13059-025-03661-z.

SummaryDeep proteomic profiling of rare cell populations has been constrained by sample input requirements. Here, we present DROPPS (droplet-based one-pot preparation for proteomic samples), an accessible low-input platform that generates high-fidelity proteomic profiles of 100–2,500 cells. By applying DROPPS within the mammary epithelium, we elucidated the connection between mitochondrial activity and clonogenicity, identifying CD36 as a marker of progenitor capacity in the basal cell compartment. We anticipate that DROPPS will accelerate biology-driven proteomic research for a multitude of rare cell populations. Graphical abstract Highlights•An accessible low-input proteomic method for rare populations of cells•Easy to implement, relying exclusively on common laboratory equipment•Performance is robust across operators and sample processing batches•Identifies CD36 as marker for mammary basal epithelial cells with progenitor capacity MotivationProteomics allows for direct measurement of cellular machinery, allowing for interrogation of a variety of biological systems. Many low-input proteomic methods only support specific study designs or require specialized equipment. To address this limitation, we have developed an accessible low-input proteomic method for studying rare populations of cells: droplet-based one-pot preparation for proteomic samples (DROPPS). Waas et al. develop and validate DROPPS, a proteomic workflow designed to democratize the capacity to profile rare cell populations without compromising data quality. DROPPS generates high-fidelity proteomic profiles from samples comprising as low as 100 cells and is amenable to facile integration with cell sorting.